Variant report

Variant	rs11548478
Chromosome Location	chr19:41247114-41247115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41221453..41223468-chr19:41246365..41247883,2	MCF-7	breast:
2	chr19:41222847..41224765-chr19:41244850..41247375,2	MCF-7	breast:
3	chr19:41237106..41239514-chr19:41244593..41247355,2	K562	blood:
4	chr19:41246510..41248162-chr19:41281990..41283890,2	K562	blood:
5	chr19:41222621..41224327-chr19:41244939..41247313,2	K562	blood:
6	chr19:41246355..41251647-chr19:41252986..41257062,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123815	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000086544	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10407351	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425765	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083566	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976551	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469427	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1870086	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1870087	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2290692	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290693	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3745210	0.90[ASN][1000 genomes]
rs3745211	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745216	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802085	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4802086	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802087	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803360	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7248468	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248570	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7251246	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7257602	0.85[AMR][1000 genomes]
rs7260405	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8111960	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11548478	C19orf54	cis	Nerve Tibial	GTEx
rs11548478	ADCK4	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart
3	chr19:41228600-41250000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:41228600-41251000	Strong transcription	Fetal Brain Female	brain
5	chr19:41229200-41247200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:41229400-41249000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:41229800-41247200	Strong transcription	Primary T cells from cord blood	blood
8	chr19:41229800-41248600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:41229800-41248600	Strong transcription	Dnd41	blood
10	chr19:41229800-41249200	Strong transcription	Thymus	Thymus
11	chr19:41229800-41250400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr19:41230400-41247200	Strong transcription	Lung	lung
13	chr19:41231600-41247400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr19:41232400-41247400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:41233600-41248400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:41233600-41249200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr19:41234800-41248400	Strong transcription	Gastric	stomach
18	chr19:41237000-41255400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:41237600-41255200	Weak transcription	Fetal Brain Male	brain
20	chr19:41238800-41248000	Strong transcription	Primary B cells from cord blood	blood
21	chr19:41239400-41250000	Strong transcription	Spleen	Spleen
22	chr19:41240200-41255600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:41241600-41251000	Weak transcription	NH-A	brain
24	chr19:41241800-41248800	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr19:41242000-41247200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:41242000-41248000	Strong transcription	HepG2	liver
27	chr19:41242000-41250600	Strong transcription	Fetal Intestine Small	intestine
28	chr19:41242000-41253800	Weak transcription	GM12878-XiMat	blood
29	chr19:41242200-41255600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:41242400-41251000	Weak transcription	Hela-S3	cervix
31	chr19:41242600-41250200	Strong transcription	Fetal Intestine Large	intestine
32	chr19:41243200-41251200	Weak transcription	Fetal Kidney	kidney
33	chr19:41243400-41248400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:41243400-41254400	Weak transcription	Psoas Muscle	Psoas
35	chr19:41243600-41247600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:41243600-41255600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr19:41243800-41247200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:41243800-41247400	Weak transcription	K562	blood
39	chr19:41243800-41248000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:41243800-41249400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr19:41243800-41255400	Weak transcription	HSMM	muscle
42	chr19:41244000-41250800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr19:41245000-41250200	Genic enhancers	Placenta	Placenta
44	chr19:41245000-41251000	Weak transcription	HUVEC	blood vessel
45	chr19:41245000-41254600	Weak transcription	Stomach Mucosa	stomach
46	chr19:41245000-41255400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr19:41245200-41248200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr19:41245200-41254400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:41245400-41247600	Genic enhancers	Brain Inferior Temporal Lobe	brain
50	chr19:41245400-41248000	Genic enhancers	Fetal Muscle Trunk	muscle

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